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davised / get_assemblies

Download assembly files from NCBI
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[10/22/24 13:06:20] WARNING Assembly 2215501 - PNUSAL000038 is being skipped due to "from large multi-isolate project". #4

Closed clb21565 closed 4 days ago

clb21565 commented 4 days ago

Hi there,

this looks awesome!

Downloaded and tested it out, but was not able to access the assemblies when running:

echo "GCA_004104335.1" | get_assemblies assembly_ids - --function genomes -o faa

The output was:

[10/22/24 13:06:17] INFO Welcome to get_assemblies v0.11.3! main.py:1226 INFO Getting assembly links. This may take a while. main.py:491 [10/22/24 13:06:19] INFO Found 1 genome(s) to download. main.py:558 INFO Expect 5 MB to 7 MB of data pending the chosen file types for download. main.py:560 INFO With 1 chunks (500 ids per), this will take around 10 secs. main.py:606 chunk ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00 [10/22/24 13:06:20] WARNING Assembly 2215501 - PNUSAL000038 is being skipped due to "from large multi-isolate project". main.py:970 docsums ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00 INFO Downloading 0 file(s).

Any suggestion?

Thanks so much!

clb21565 commented 4 days ago

Nevermind :-] this is in the docs...

--keepmulti By default, genomes from large multi-isolate studies are removed.